Before modification (adding false easting and northing), in QGIS, I inserted a shp layer (same source) twice but assigned them to two different CRS for testing (one to EPSG:29873, and the other one to user defined USER:100001, Basemap using Bing Aerial with project CSR to EPSG:3857 WGS84/Pseudo Mercator). the result displayed quite surprisingly. the EPSG:298873 CRS locate the shp file correctly but NOT the user defined custom CRS (300+++ Km toward north from the correct one)! In fact they should displayed at the same location right, seeing that they are using the same Proj4 parameters!!!

At first glance, the Datum D_Timbalai_1948 is missing. So you might have lost the +towgs84 parameters. Also, the projection parameters are different. Is the newly saved Shapefile displaced as well?
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AndreJJan 11 '13 at 9:26

Which shapefile aligns with Openlayers background, if project CRS is set to EPSG:3857?
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AndreJJan 11 '13 at 9:38

1 Answer
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I tried the same as you did, and could not replicate the error. But encountered that Qgis sometimes uses another CRS than that stored in the prj file. So take care which CRS is applied to the loaded layers. I did some grids in both 29873 and user defined (red), and they match perfectly.

Your proj string misses the gamma value. Thats the crazy thing about omerc: The projection axis is not a meridian (as most other merc projections), but with an angle to it. The coordinates are finally reprojected to have north up again. The SR string is even older, and misses the +towgs84 also.

The grid with my proj string in black and yours in red looks like this:

You have taken the proj string from QGIS Lisboa, probably Windows standalone installer. There is a bug in that installer, which prevents QGIS from synchronizing with the built-in GDAL projection database. Installing in a path without blanks (that is not in C:\Programs (x86)\ solves that issue, or using OSGEO4W installer. Master is only available with the later one.

Earlier versions of GDAL had a different way of handling the omerc projection, which was found to be inaccurate, and replaced with the handling of the gamma value. But now you have a new version of GDAL built inside QGIS, but the old proj string in the not-updated CRS database.

You can modify the CRS database, called srs.db, with spatialite GUI (because its a sqlite database as well), or reinstall QGIS to have correct handling of EPSG:29873.

i insert few dumpscreen into original post to show how i create the custom user defined CRS. please kindly help to inspect and hopefully i get the right procedure to do it.
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LUKIPJan 12 '13 at 1:38

i try using spatial reference tool to generate the Proj4 format for Timbalai 1948/ RSO Borneo (m) +proj=omerc +lat_0=4 +lonc=115 +alpha=53.31582047222222 +k=0.99984 +x_0=590476.87 +y_0=442857.65 +ellps=evrstSS +units=m +no_defs and assigned the shapefile to this new custom CRS. the output still cannot match the two CRS together. the new user defined CRS using spatial reference tool still go to North 300,+++Km
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LUKIPJan 12 '13 at 2:25

OK, no I got the differences, see my extended answer. By the way, your proj string has the correct false easting and northing already!
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AndreJJan 12 '13 at 6:21

thanks for all the help, my layers locating at correct position now. for the 2000000, 5000000 false easting and northing, i modified your Proj4 format to +x_0=2590476.87 +y_0=5442857.65 and it display correctly as well.
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LUKIPJan 14 '13 at 6:38

any good tool apart from spatial reference to generate the proj4 string from WKT format for use in GIS FOSS?
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LUKIPJan 16 '13 at 0:24